cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i HCC1395_BL.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz HCC1395_BL.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL HCC1395_BL.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments HCC1395_BL.tnseq_tumor_only.segments HCC1395_BL.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:14512344, elapsed 0.2s, est remaining 4.0s, peak mem 147MB, user 0.6s, sys 0.1s, output queue size 53
progress 10% @chr21:25714540, elapsed 0.3s, est remaining 2.9s, peak mem 158MB, user 1.5s, sys 0.1s, output queue size 106
progress 15% @chr21:29038926, elapsed 0.4s, est remaining 2.4s, peak mem 162MB, user 2.3s, sys 0.1s, output queue size 23
progress 20% @chr21:30479945, elapsed 0.5s, est remaining 2.0s, peak mem 166MB, user 3.0s, sys 0.2s, output queue size 16
progress 25% @chr21:32359696, elapsed 0.6s, est remaining 1.8s, peak mem 169MB, user 3.8s, sys 0.2s, output queue size 64
progress 30% @chr21:33355216, elapsed 0.7s, est remaining 1.7s, peak mem 171MB, user 4.6s, sys 0.2s, output queue size 23
progress 35% @chr21:34385378, elapsed 0.9s, est remaining 1.6s, peak mem 175MB, user 5.4s, sys 0.2s, output queue size 74
progress 40% @chr21:33549376, elapsed 1.2s, est remaining 1.7s, peak mem 225MB, user 6.5s, sys 0.3s, output queue size 163
progress 45% @chr21:37186949, elapsed 1.3s, est remaining 1.6s, peak mem 232MB, user 7.4s, sys 0.3s, output queue size 165
progress 50% @chr21:39250696, elapsed 1.6s, est remaining 1.6s, peak mem 244MB, user 8.5s, sys 0.4s, output queue size 264
progress 55% @chr21:41436915, elapsed 1.7s, est remaining 1.4s, peak mem 256MB, user 9.4s, sys 0.4s, output queue size 370
progress 60% @chr21:41766760, elapsed 2.9s, est remaining 1.9s, peak mem 387MB, user 15.0s, sys 0.5s, output queue size 16
progress 65% @chr21:42442352, elapsed 3.0s, est remaining 1.6s, peak mem 387MB, user 16.7s, sys 0.6s, output queue size 123
progress 70% @chr21:41497033, elapsed 3.1s, est remaining 1.3s, peak mem 394MB, user 18.3s, sys 0.6s, output queue size 223
progress 75% @chr21:44120248, elapsed 3.2s, est remaining 1.1s, peak mem 394MB, user 19.1s, sys 0.7s, output queue size 327
progress 80% @chr21:44413791, elapsed 3.4s, est remaining 0.8s, peak mem 397MB, user 20.3s, sys 0.7s, output queue size 429
progress 85% @chr21:45183262, elapsed 3.5s, est remaining 0.6s, peak mem 397MB, user 21.3s, sys 0.7s, output queue size 505
progress 90% @chr21:45998797, elapsed 3.7s, est remaining 0.4s, peak mem 397MB, user 22.8s, sys 0.7s, output queue size 612
progress 95% @chr21:46356874, elapsed 3.8s, est remaining 0.2s, peak mem 397MB, user 23.9s, sys 0.8s, output queue size 720
progress 100% @chr21:46661700, elapsed 4.0s, est remaining 0.0s, peak mem 397MB, user 25.7s, sys 0.8s, output queue size 29
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000606a6
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef 40417f5e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 128
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 163002590
output file size: 51811
reads: 1955548
contig: 1979 intervals 801713 bases
"assemble": 227 calls 1.069 user 0.011 sys 1.728 real
"assemble_addRead": 227 calls 0.020 user 0.000 sys 0.043 real
"assemble_buildGraph": 511 calls 0.415 user 0.000 sys 0.771 real
"assemble_computecigar": 321 calls 0.268 user 0.040 sys 0.388 real
"assemble_kg_build_calcsize": 511 calls 0.268 user 0.000 sys 0.432 real
"assemble_kg_build_clear": 699 calls 0.060 user 0.000 sys 0.063 real
"assemble_kg_build_prepare": 1022 calls 0.291 user 0.010 sys 0.412 real
"assemble_kg_build_threading": 323 calls 0.137 user 0.000 sys 0.322 real
"assemble_kg_op1": 323 calls 0.129 user 0.000 sys 0.231 real
"assemble_kg_op2": 323 calls 0.030 user 0.000 sys 0.018 real
"assemble_kg_op3": 323 calls 0.020 user 0.000 sys 0.007 real
"assemble_sg_clean": 321 calls 0.000 user 0.000 sys 0.051 real
"assemble_sg_create": 321 calls 0.064 user 0.000 sys 0.091 real
"checkGraph": 227 calls 0.010 user 0.000 sys 0.001 real
"findHaplotype": 227 calls 0.288 user 0.040 sys 0.402 real
advance: 2074 calls 8.100 user 0.284 sys 11.793 real
assemble_region: 227 calls 1.387 user 0.060 sys 2.188 real
build_pileup: 1957 calls 0.040 user 0.010 sys 0.106 real
build_stats: 1979 calls 2.417 user 0.130 sys 3.666 real
build_variants: 179 calls 0.000 user 0.000 sys 0.002 real
calc: 3869 calls 1.454 user 0.001 sys 2.036 real
calc_region: 179 calls 5.932 user 0.012 sys 8.735 real
call_region: 179 calls 0.115 user 0.000 sys 0.162 real
clip_region: 406 calls 0.150 user 0.000 sys 0.132 real
done: 1 calls 1.030 user 0.000 sys 1.041 real
execute: 1 calls 0.008 user 0.001 sys 4.077 real
fetch: 8147 calls 1.719 user 0.022 sys 2.473 real
fetch_ref: 8428 calls 0.059 user 0.030 sys 0.155 real
fetch_region: 227 calls 0.040 user 0.000 sys 0.049 real
fetch_vcf: 2074 calls 1.003 user 0.048 sys 1.385 real
idle: 52 calls 0.070 user 0.001 sys 25.897 real
init: 1 calls 0.100 user 0.000 sys 0.105 real
pairhmm: 1058 calls 11.623 user 0.020 sys 15.832 real
realign: 179 calls 0.901 user 0.000 sys 1.380 real
region: 4053 calls 7.428 user 0.081 sys 11.065 real
tracker: 4053 calls 0.024 user 0.000 sys 0.032 real
trim_region: 227 calls 0.010 user 0.000 sys 0.004 real
overall: 417304576 mem 34.752 user 0.987 sys 6.508 real